Thank you for posting and welcome to the community.
I'm sorry to see you've been running into issues attempting to program your Bose remote to control your Dish Hopper 3, but I'll be happy to help.
The reason why you're unable to control it at this time is that the Dish Hopper 3 is set to be controlled using RF signals instead of IR. However, you can change this in the settings menu of your Dish Hopper to accept IR commands.
Once you have the changed the settings to accept IR commands, I would suggest trying to reprogram the Bose remote.
Let us know if you have any other questions.
Joel - Community Support
Thanks for the additional information! It seems most likely that the problem is centered around the IR receiver in the Hopper 3 not being able to "see" the signal. If you locate the position of the IR sensor in the Hopper 3 and place it such that it's in direct line of sight with your viewing position, does that improve communication? Also, if you are using a glass table or other reflective surface you might try pulling the Hopper 3 out to the edge to help prevent additional interference.
Let us know what you find!
Greg - Community Support